Genome-Wide Investigation and Analysis of Microsatellites and Compound Microsatellites in Leptolyngbya-like Species, Cyanobacteria
Abstract
:1. Introduction
2. Materials and Methods
2.1. Genome Sequences
2.2. Identification and Analysis of SSRs and CSSRs
2.3. Statistical Analysis
3. Results
3.1. Phylogenetic Relationship of Leptolyngbya Strains
3.2. Number, Relative Abundance and Density of SSRs and CSSRs
3.3. Distribution and Diversity of SSRs
3.4. Complexity, Motifs and Distribution of CSSRs
3.5. Correlation Analysis
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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No. | Species Name | Isolation Source | Size (bp) | GC (%) | SSR | CSSR | |||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
nSSR a | RA b | RD c | nCSSR d | RA b | RD c | ncSSR e | cSSR% f | Z Score g | |||||
S1 | Leptolyngbya boryana NIES-2135 | N/A | 6,255,462 | 47.02 | 15,780 | 2.52 | 16.64 | 489 | 0.08 | 1.05 | 1006 | 6.38 | 0.13 |
S2 | Leptolyngbya boryana PCC 6306 | USA | 7,262,454 | 47.02 | 17,953 | 2.47 | 16.30 | 538 | 0.07 | 1.01 | 1110 | 6.19 | 0.07 |
S3 | Leptolyngbya boryana dg5 | N/A | 6,176,364 | 46.99 | 15,600 | 2.53 | 16.67 | 485 | 0.08 | 1.06 | 1001 | 6.42 | 0.06 |
S4 | Leptolyngbya sp. FACHB-161 | China | 6,743,911 | 46.97 | 16,858 | 2.50 | 16.49 | 513 | 0.08 | 1.03 | 1061 | 6.3 | 0.01 |
S5 | Leptolyngbya sp. FACHB-238 | Freshwater, China | 7,173,154 | 46.98 | 17,775 | 2.48 | 16.33 | 539 | 0.08 | 1.02 | 1113 | 6.27 | 0.05 |
S6 | Leptolyngbya sp. FACHB-239 | Terrestrial, China | 7,147,343 | 46.98 | 17,716 | 2.48 | 16.34 | 539 | 0.08 | 1.02 | 1113 | 6.29 | 0.05 |
S7 | Leptolyngbya sp. FACHB-402 | Freshwater, China | 7,138,201 | 46.98 | 17,693 | 2.48 | 16.34 | 539 | 0.08 | 1.03 | 1113 | 6.3 | 0.05 |
S8 | Leptolyngbya boryana IAM M-101 | N/A | 6,176,363 | 46.99 | 15,600 | 2.53 | 16.67 | 485 | 0.08 | 1.06 | 1001 | 6.42 | 0.06 |
S9 | Leptolyngbya sp. UWPOB_LEPTO1 | Activated sludge, Wisconsin, USA | 6,800,371 | 46.86 | 16,881 | 2.48 | 16.36 | 489 | 0.07 | 0.98 | 1007 | 5.97 | 0.11 |
S10 | Leptolyngbya sp. FACHB-1624 | Freshwater, China | 6,648,037 | 46.89 | 16,537 | 2.49 | 16.41 | 476 | 0.07 | 0.96 | 972 | 5.88 | 0.29 |
S11 | Leptolyngbya sp. FACHB-17 | Freshwater, China | 5,574,121 | 48.17 | 11,970 | 2.15 | 14.28 | 303 | 0.05 | 0.74 | 617 | 5.16 | 0.28 |
S12 | Leptolyngbya sp. NIES-2104 | Biofilm, terrestrial, Japan | 6,386,309 | 47.43 | 13,034 | 2.04 | 13.44 | 309 | 0.05 | 0.65 | 631 | 4.85 | 0.23 |
S13 | Leptolyngbya sp. NIES-3755 | Soil, Japan | 6,244,811 | 46.65 | 12,513 | 2.00 | 13.20 | 286 | 0.05 | 0.61 | 580 | 4.64 | 0.34 |
S14 | Leptolyngbya sp. FACHB-321 | Terrestrial, China | 6,715,002 | 49.97 | 15,990 | 2.38 | 16.10 | 497 | 0.07 | 1.02 | 1017 | 6.37 | 0.25 |
S15 | Leptolyngbya sp. ULC077bin1 | Microbial mat, Canada | 5,462,880 | 48.17 | 14,135 | 2.59 | 17.25 | 397 | 0.07 | 0.99 | 815 | 5.77 | 0.16 |
S16 | Leptolyngbya sp. ‘hensonii’ | Pinnacle phototroph mat, Florida, USA | 5,940,029 | 52.32 | 14,206 | 2.39 | 16.01 | 433 | 0.07 | 1.00 | 886 | 6.24 | 0.23 |
S17 | Leptolyngbya sp. FACHB-8 | Freshwater, China | 6,927,450 | 50.67 | 17,792 | 2.57 | 16.93 | 625 | 0.09 | 1.21 | 1295 | 7.28 | −0.03 |
S18 | Leptolyngbya sp. FACHB-16 | Freshwater, China | 8,006,770 | 50.32 | 20,514 | 2.56 | 16.89 | 726 | 0.09 | 1.22 | 1509 | 7.36 | −0.12 |
S19 | Leptolyngbya ohadii IS1 | Biological soil crust, Nitzana, Israel | 7,902,459 | 52.09 | 17,477 | 2.21 | 15.29 | 644 | 0.08 | 1.15 | 1357 | 7.77 | −0.46 |
S20 | Leptolyngbya sp. JSC-1 | La Duke Hot Springs, Montana, USA | 7,866,824 | 50.72 | 15,873 | 2.09 | 14.41 | 537 | 0.07 | 1.03 | 1183 | 7.46 | −1.45 |
S21 | Leptolyngbya sp. IPPAS B-1204 | Lake water, Lake Tolbo Nuur, Mongolia | 8,174,684 | 50.83 | 16,980 | 2.08 | 14.33 | 538 | 0.07 | 0.96 | 1165 | 6.87 | −1.05 |
S22 | Leptolyngbya sp. DLM2.Bin15 | Alkaline salt lake, Cariboo Plateau, Canada | 5,006,105 | 53.93 | 11,640 | 2.33 | 16.29 | 366 | 0.07 | 1.08 | 759 | 6.53 | −0.04 |
S23 | Leptolyngbya sp. CCY15150 | North Sea beach, Schiermonikoog, Netherlands | 5,756,177 | 53.40 | 13,178 | 2.29 | 15.98 | 381 | 0.07 | 0.96 | 781 | 5.93 | 0.18 |
S24 | Leptolyngbya cf. ectocarpi LEGE 11,479 | Diving spot near Leixes Harbour, Portugal | 6,774,485 | 49.35 | 19,842 | 2.93 | 19.64 | 726 | 0.11 | 1.46 | 1482 | 7.47 | 0.37 |
S25 | Leptolyngbya sp. Heron Island J | Heron Island, Australia | 8,064,167 | 48.05 | 22,589 | 2.80 | 18.77 | 800 | 0.10 | 1.37 | 1646 | 7.29 | 0.16 |
S26 | Leptolyngbya sp. SIO4C1 | Stromatolite, Millennium Atoll, Pacific Ocean | 5,299,754 | 54.81 | 16,272 | 3.07 | 21.33 | 598 | 0.11 | 1.63 | 1240 | 7.63 | −0.05 |
S27 | Leptolyngbya sp. BC1307 | Lake Hoare margin, microbial mat, Antarctica | 4,916,582 | 52.93 | 15,073 | 3.07 | 20.91 | 578 | 0.12 | 1.64 | 1180 | 7.83 | 0.33 |
S28 | Leptolyngbya foveolarum ULC129bin1 | Microbial mat, Antarctica | 4,750,982 | 51.01 | 13,708 | 2.89 | 19.52 | 463 | 0.10 | 1.37 | 955 | 6.97 | 0.07 |
S29 | Leptolyngbya sp. SIO1E4 | Samoa, marine benthic turfs, American | 8,792,215 | 51.44 | 24,000 | 2.73 | 18.19 | 907 | 0.10 | 1.43 | 1865 | 7.78 | 0.19 |
S30 | Leptolyngbya sp. SIO1D8 | Portobelo marine benthic turfs, Panama | 7,757,311 | 47.92 | 20,287 | 2.62 | 17.41 | 695 | 0.09 | 1.23 | 1428 | 7.04 | 0.19 |
S31 | Leptolyngbya sp. SIOISBB | Marine benthic turfs, Indonesia | 8,337,037 | 51.86 | 21,217 | 2.55 | 17.06 | 698 | 0.08 | 1.17 | 1441 | 6.8 | 0.06 |
S32 | Leptolyngbya sp. RL_3_1 | Stromatolite, Cape Recife, South Africa | 3,943,200 | 56.13 | 11,086 | 2.81 | 19.44 | 384 | 0.10 | 1.40 | 796 | 7.19 | −0.03 |
S33 | Leptolyngbya sp. LCM1.Bin17 | Alkaline salt lake, Cariboo Plateau, Canada | 4,618,091 | 55.39 | 12,930 | 2.80 | 19.44 | 507 | 0.11 | 1.60 | 1050 | 8.13 | −0.02 |
S34 | Leptolyngbya sp. BL0902 | Imperial Valley, California, USA | 4,710,209 | 57.65 | 12,530 | 2.66 | 19.04 | 418 | 0.09 | 1.31 | 866 | 6.92 | −0.02 |
S35 | Leptolyngbya sp. KIOST-1 | Culture pond, Ansan, South Korea | 6,320,122 | 59.44 | 19,308 | 3.06 | 22.05 | 788 | 0.12 | 1.88 | 1642 | 8.51 | −0.19 |
S36 | Leptolyngbya sp. ULC186bin1 | Microbial mat, Belgium | 5,080,999 | 57.41 | 14,809 | 2.92 | 20.70 | 564 | 0.11 | 1.66 | 1185 | 8.01 | −0.36 |
S37 | Leptolyngbya sp. FACHB-60 | Freshwater, China | 5,913,379 | 55.56 | 16,386 | 2.77 | 19.33 | 609 | 0.10 | 1.48 | 1246 | 7.61 | 0.28 |
S38 | Leptolyngbya sp. DLM2.Bin27 | Alkaline salt lake, Cariboo Plateau, Canada | 4,277,754 | 59.01 | 14,185 | 3.32 | 24.08 | 585 | 0.14 | 2.06 | 1214 | 8.56 | −0.07 |
S39 | Leptolyngbya sp. ULC073bin1 | Microbial mat, Antarctica | 4,608,713 | 57.79 | 14,600 | 3.17 | 22.73 | 616 | 0.13 | 2.03 | 1312 | 8.99 | −0.72 |
S40 | Leptolyngbya antarctica ULC041bin1 | Microbial mat, Antarctica | 4,711,992 | 58.22 | 15,225 | 3.23 | 23.31 | 654 | 0.14 | 2.11 | 1380 | 9.07 | −0.50 |
S41 | Leptolyngbya sp. 7M | Thermal spring, Miravalles, Costa Rica | 6,990,850 | 49.92 | 15,706 | 2.25 | 15.09 | 428 | 0.06 | 0.83 | 875 | 5.58 | 0.25 |
S42 | Leptolyngbya sp. AVDCRST_MAG94 | Avdat LTER, Negev Desert, Israel | 5,510,397 | 52.11 | 13,152 | 2.39 | 16.45 | 378 | 0.07 | 0.98 | 770 | 5.86 | 0.31 |
S43 | Leptolyngbya sp. ES-bin-22 | Knuths Fjeld, Little Firn glacier, Greenland | 5,129,489 | 51.62 | 12,342 | 2.41 | 16.29 | 352 | 0.07 | 0.96 | 735 | 5.96 | −0.17 |
S44 | Leptolyngbya sp. FACHB-711 | Freshwater, China | 6,345,842 | 50.70 | 14,268 | 2.25 | 15.41 | 452 | 0.07 | 1.01 | 931 | 6.53 | 0.10 |
S45 | Leptolyngbya sp. SIO3F4 | Marine benthic turfs, Boco del Toro, Panama | 8,111,628 | 45.71 | 23,151 | 2.85 | 19.06 | 873 | 0.11 | 1.47 | 1801 | 7.78 | 0.09 |
S46 | Leptolyngbya sp. SIO4C5 | Stromatolite, Marion Bay Southeast, Australia | 5,604,438 | 53.04 | 14,754 | 2.63 | 18.26 | 496 | 0.09 | 1.28 | 1027 | 6.97 | −0.01 |
Genome Size | GC Content | nSSR | ncSSR | ||
---|---|---|---|---|---|
nSSR | ρ | 0.81 | −0.30 | - | 0.88 |
Significance | p < 0.01 | p < 0.05 | - | p < 0.01 | |
nCSSR | ρ | 0.52 | 0.11 | 0.89 | 1.00 |
Significance | p < 0.01 | p > 0.05 | p < 0.01 | p < 0.01 |
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Yao, D.; Cheng, L.; Du, L.; Li, M.; Daroch, M.; Tang, J. Genome-Wide Investigation and Analysis of Microsatellites and Compound Microsatellites in Leptolyngbya-like Species, Cyanobacteria. Life 2021, 11, 1258. https://doi.org/10.3390/life11111258
Yao D, Cheng L, Du L, Li M, Daroch M, Tang J. Genome-Wide Investigation and Analysis of Microsatellites and Compound Microsatellites in Leptolyngbya-like Species, Cyanobacteria. Life. 2021; 11(11):1258. https://doi.org/10.3390/life11111258
Chicago/Turabian StyleYao, Dan, Lei Cheng, Lianming Du, Meijin Li, Maurycy Daroch, and Jie Tang. 2021. "Genome-Wide Investigation and Analysis of Microsatellites and Compound Microsatellites in Leptolyngbya-like Species, Cyanobacteria" Life 11, no. 11: 1258. https://doi.org/10.3390/life11111258